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PEAKS Studio result visualization #12
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We haven't tested the pepXML and mzXML from PEAKS Studio. It looks PEAKS Studio can export mzIdentML which is a more standard format. Could you give a try using mzIdentML instead of pepXML? |
If you can share the pepXML and mzXML files with us, we can do a test on the data. |
Could you share the files with us by dropbox or google drive? |
Here is a link to google drive folder: https://drive.google.com/drive/folders/15O2b6l85fsmCGHNu4Oei4xp-r2MGzpgc?usp=sharing Not sure if this is useful to know, but the .mzXML is still in resolution mode display. |
Thanks JC. I will take a look and test it today. Kai |
The raw MS data is imported into PEAKS. Then the software converts and exports it for further analysis (in my case Skyline). However, the lack of charge information might be an instrumentation issues. This data was acquired with a Synapt G2-Si TOF (Waters) instrument. For whatever reason, the precursor charge annotation is VERY PROBLEMATIC and doesn't seem to be written on the file (I think) since whenever I try to convert it with msconvert I usually don't get a useful charge annotation. I can only get the charge recalculation using Proteowizards "turbocharger" "filter" for raw data that didn't use IMS. The pepXML has the "assumed" charge annotated since PEAKS re-estimate the charge state using the MS1 traces. However, to fill the "precursorScanNum" and "precursorIntensity" I am not entirely sure how to fill that or if it would be written in the raw file. |
Could you please share the raw file with me? |
PEAKS Studio can also export MGF. We could try MGF to see if it works |
I just uploaded the raw data and the mgf file exported from PEAKS Studio (this format has the charge state written) in the shared folder |
Btw, the raw file had IMS separation of fragment ions so it doesn't work nicely in msconvert (at least what I have tried). If you manage to get a useful .mzXML or .mgf from a conversion of the raw file I would be very curious to learn how |
Kai! Thanks a lot! You are awesome for all the time invested into this! Indeed, it was a database search of 6 files. Sorry for not pointing out this and I apologize if it made you waste time unnecessarily. So I went ahead and tested your suggestions with the names that should be allocated and realized that PDV can fully support the .mzid and .mgf exports from PEAKS! HOWEVER, you have to pay attention from where the exports are performed since the .mzid file names are written differently: File names are written with .mgf suffix if exported "For Scaffold" option: File names are written with original file suffix (i.e. "raw" for this Waters data) if exported from the "generic" exports section (this is the one I sent you last time....oops): I hope that this clarification is useful for you or future users. One comment on the results is that although the peptide annottation seems to be working well, the retention time and precursor m/z assignment is off. All RT and "m/z" rows are labelled as "-0.0". The RT in the .mgf files is written in seconds. Could it be an issue of units conversion? However, for the m/z I have no idea. I have uploaded the Scaffold exported .mzid file and .mgf files in case you would like to look further into it. Last questions, with respect to number of PTMS and reporter ions since this is the actual application I would like to test for the app. I routinely look for 30+ modifications that have modification specific modifications with PEAKS. Are there any limits with the number of modifications that can be considered? Can reporter ions or specific neutral losses be considered as ions to be mapped? Thanks for your time and help! |
Hi PDV community,
I was trying to visualize some .pepXML results and .mzXML files exported from PEAKS Studio 10.5.
However, I am receiving an error (attached image) that is preventing me to do any visualization. My computer is german and the decimal delimiters ("," for Germany) is the only thing that comes to mind...
Any suggestions for how to fix this? I was very curious to explore the visualization/annotation of PDV for peptides carrying PTMs not present in unimod.
Sincerely,
JC
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